FOXN2

protein-coding

forkhead box N2, the group of Forkhead boxes

Gene summary

This gene encodes a forkhead domain binding protein and may function in the transcriptional regulation of the human T-cell leukemia virus long terminal repeat. [provided by RefSeq, Jul 2008]

Previous symbols:

HTLF

MANE transcript

NM_002158.4

Inheritance

—

ClinVar variants

U:69B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.21

Max pathogenic AF

—

Genomic locus

chr2:48,314,637-48,379,295

External References & Databases

Ensembl (ENSG00000170802)

Transcript & Mutation Effects

hg38 • Region Span ~64.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FOXN2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 67

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002158.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		2 clinvar	3
missense			65 clinvar	2 clinvar		67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	69	2	2	73

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 64 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002158.4	RefSeq	NP_002149.2	5	MANE Select
ENST00000340553.8	Ensembl	ENSP00000343633.3	5	MANE Select
NM_001375442.1	RefSeq	NP_001362371.1	5	Standard
NM_001375443.1	RefSeq	NP_001362372.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
skeletal muscle cell differentiation

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription factor activity
protein binding
sequence-specific DNA binding

Cellular Component

nucleus
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000340553
Coding exons: 5
Length: 64658
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125743
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.587	254	229	1.11	0.0000112	2835
Missense (PolyPhen)		63	72.537	0.86852		931
Synonymous	-0.633	89	81.7	1.09	0.00000416	819
Loss of Function	3.21	4	19.2	0.209	0.00000114	228

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0.00017	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds to the purine-rich region in HTLV-I LTR.;

Recessive Scores

pRec: 0.165

Intolerance Scores

LoFtool: 0.123
RVIS EVS: -0.74
RVIS percentile EVS: 13.94

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.996

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium